Comparison of solid tissue sequencing and liquid biopsy accuracy in identification of clinically relevant gene mutations and rearrangements in lung adenocarcinomas

Liquid biopsy has emerged as an alternative source of nucleic acids for the management of Epidermal Growth Factor Receptor (EGFR)-mutant non-Small Cell Lung Cancer (NSCLC). The use of circulating cell-free DNA (cfDNA) has been recently introduced in clinical practice, resulting in the improvement of the identification of druggable EGFR mutations for the diagnosis and monitoring of response to targeted therapy. EGFR-dependent (T790M and C797S mutations) and independent (Mesenchymal Epithelial Transition [MET] gene amplification, Kirsten Rat Sarcoma [KRAS], Phosphatidyl-Inositol 4,5-bisphosphate 3-Kinase Catalytic subunit Alpha isoform [PI3KCA], and RAF murine sarcoma viral oncogene homolog B1 [BRAF] gene mutations) mechanisms of resistance to EGFR tyrosine kinase inhibitors (TKIs) have been evaluated in plasma samples from NSCLC patients using highly sensitive methods (i.e., digital droplet PCR, Next Generation Sequencing), allowing for the switch to other therapies. Therefore, liquid biopsy is a non-invasive method able to detect the molecular dynamic changes that occur under the pressure of treatment, and to capture tumor heterogeneity more efficiently than is allowed by tissue biopsy. This review addresses how liquid biopsy may be used to guide the choice of treatment strategy in EGFR-mutant NSCLC.

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Abstract 2729: Development of a targeted liquid biopsy for early gynecologic cancer detection leads to discovery of a highly prevalent genomic landscape of cancer driver gene mutations in uterine tissue from women without cancer

10.1158/1538-7445.am2019-2729 ◽

2019 ◽

Author(s):

Deep S. Pandya ◽

Shannon Tomita ◽

Olga Camacho ◽

Sabina Swierczek ◽

Catalina Camacho ◽

...

Keyword(s):

Cancer Detection ◽

Liquid Biopsy ◽

Gynecologic Cancer ◽

Gene Mutations ◽

Driver Gene ◽

Uterine Tissue ◽

Cancer Driver ◽

Cancer Driver Gene ◽

Genomic Landscape

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Rapid Polymerase Chain Reaction-Based Detection of Epidermal Growth Factor Receptor Gene Mutations in Lung Adenocarcinomas

Journal of Molecular Diagnostics ◽

10.1016/s1525-1578(10)60569-7 ◽

2005 ◽

Vol 7 (3) ◽

pp. 396-403 ◽

Cited By ~ 189

Author(s):

Qiulu Pan ◽

William Pao ◽

Marc Ladanyi

Keyword(s):

Polymerase Chain Reaction ◽

Epidermal Growth Factor Receptor ◽

Receptor Gene ◽

Growth Factor Receptor ◽

Gene Mutations ◽

Chain Reaction ◽

Rapid Polymerase Chain Reaction ◽

Epidermal Growth ◽

Polymerase Chain ◽

Lung Adenocarcinomas

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Clinicopathological, Radiological, and Molecular Features of Primary Lung Adenocarcinoma with Morule-Like Components

Disease Markers ◽

10.1155/2021/9186056 ◽

2021 ◽

Vol 2021 ◽

pp. 1-10

Author(s):

Li-Li Wang ◽

Li Ding ◽

Peng Zhao ◽

Jing-Jing Guan ◽

Xiao-Bin Ji ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Egfr Mutation ◽

Pik3ca Mutation ◽

Gene Mutations ◽

Invasive Adenocarcinoma ◽

Targeted Next Generation Sequencing ◽

Molecular Features ◽

Solid Nodule ◽

Primary Lung Adenocarcinoma ◽

Lung Adenocarcinomas

Background. Morule-like component (MLC) was a rare structure in primary lung adenocarcinoma. We aimed to reveal the clinicopathological, radiological, immunohistochemical, and molecular features of lung adenocarcinoma with MLCs. Methods. Twenty lung adenocarcinomas with MLCs were collected, and computed tomographic and histological documents were reviewed. Immunohistochemistry, targeted next-generation sequencing, and Sanger sequencing for β-catenin gene were performed. Results. There were 9 lepidic adenocarcinomas, 8 acinar adenocarcinomas, 2 papillary adenocarcinomas, and 1 minimally invasive adenocarcinoma. Most patients (16/17) were shown a pure solid nodule, and 1 patient was shown a partly solid nodule on chest computed tomography (CT). Nine cases were accompanied with micropapillary components, and 3 were with cribriform components in which 2 suffered a worse prognosis. No significant association was found between the MCLs and the overall survival of lung adenocarcinoma ( P = 0.109 ). The MLCs were often arranged in whorled or streaming patterns. The cells in MLCs showed syncytial and mild appearance. The MLCs were positive for E-cadherin, CK7, TTF-1, napsin-A, vimentin, and β-catenin (membrane), and negative for CK5/6, p40, p63, Synaptophysin, chromogranin A, and Cdx-2. EGFR mutation, ALK-EML4 fusion, HER2 amplification, and PIK3CA mutation were detected in 16 cases, 2 cases, 1 case, and 1 case, respectively. EGFR mutation was more frequent in adenocarcinomas with MLCs than those without MLCs ( P = 0.040 ). β-catenin gene mutation was not detected in any patients. Conclusions. MLC is often observed in the background of acinar, lepidic, and papillary adenocarcinomas. Lung adenocarcinomas with MLCs tend to appear as a solid mass on CT and harbor EGFR gene mutations. The micropapillary components and cribriform components may cause poor prognosis of lung adenocarcinomas with MLCs. Vimentin is always positive in MLCs, and it is a useful marker for the identification of MLCs.

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TECHNICAL ASPECTS OF LIQUID BIOPSY: INFLUENCE OF PREANALYTICAL PARAMETERS ON THE CONCENTRATION OF CIRCULATING TUMOR DNA IN PLASMA OF CANCER PATIENTS

Problems in oncology ◽

10.37469/0507-3758-2020-66-4-391-397 ◽

2020 ◽

Vol 66 (4) ◽

pp. 391-397

Author(s):

T. Sokolova ◽

T. Laidus ◽

R. Meerovich ◽

K. Zagorodnev ◽

Aleksandr Martyanov ◽

...

Keyword(s):

Liquid Biopsy ◽

Distant Metastases ◽

Circulating Tumor Dna ◽

Cancer Diagnostics ◽

Braf V600e ◽

Nucleotide Substitutions ◽

Non Invasive ◽

Intrapatient Variability ◽

Lung Adenocarcinomas ◽

Tumor Dna

«Liquid biopsy» is gradually becoming a mandatory procedure in cancer diagnostics. The aim of this procedure is to detect and monitor tumor-specific markers in various body fluids (blood, urine, pleural fluid, etc.). Significant efforts have been made to convert the most common mutational tests (EGFR, KRAS, BRAF) into non-invasive procedures. Despite some advantages, “liquid biopsy” is still not equivalent to traditional tissue analysis due to limited sensitivity and specificity; it cannot be routinely used in cancer medicine until the standardization of pre-analytical procedures is agreed. We intend to improve the performance of liquid biopsy for detection of a number of clinically relevant mutations (EGFR: ex19del and L858R; KRAS: 12, 13, 61, 146 codon nucleotide substitutions; BRAF: V600E). 417 plasma samples obtained from 88 patients (KRAS/NRAS/BRAF-mutated colorectal cancer (CRC): n= 57; EGFR-mutated lung adenocarcinomas (LC): n = 14; BRAF-mutated melanoma: n = 17) were analyzed by ddPCR for the presence of corresponding mutations in the circulating tumor DNA (ctDNA). Presence of tumor-specific mutations in plasma was confirmed in 32/57 (56%) CRC, 7/14 (50%) LC, and 4/17 (24%) melanoma cases. The proportion of mutation-positive plasma cases was tended to be higher in the group of patients with distant metastases compared to subjects with localized disease [34/56 (61%) vs. 5/15 (33%), р = 0.058]. 86 patients provided their blood at 9.00 (morning) and at 16.00 (afternoon). In addition, blood-takes were performed before and 15 minutes after usual breakfast as well as before and 15 minutes after moderate physical exercise. The detection rate of cancer-specific mutations in plasma was not significantly correlated with described above circumstances of blood-take. Meanwhile, the noticeable intrapatient variability of circulating mutation success rate has been detected. Thus, depending on clinical circumstances, at least negative ctDNA tests could be advised to be repeated in some patients, in order to ensure the reliability of results.

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Incidence of Androgen Receptor and DNA Repair Gene Mutations in Advanced Solid Malignancies: Clinical Impact of Liquid Biopsy at Veteran Affairs Medical Center

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqaa161.318 ◽

2020 ◽

Vol 154 (Supplement_1) ◽

pp. S145-S146

Author(s):

S Dalal ◽

D Jhala

Keyword(s):

Dna Repair ◽

Liquid Biopsy ◽

Medical Center ◽

Gene Mutations ◽

Genetic Mutations ◽

Precision Oncology ◽

Liquid Biopsies ◽

Repair Gene ◽

Solid Malignancies ◽

Dna Repair Gene

Abstract Introduction/Objective The advent of Liquid biopsy targeting genetic mutations in solid tumors is a major milestone in field of precision oncology. This minimally invasive, novel revolutionary technique analyses circulating tumor cells (CTC) in peripheral blood and detects signature genomic alterations. DNA repair gene (DDR) mutations have been reported in 25-40% of prostatic cancers and >50% of non-small cell lung cancers (NSCLC), being more common in late-stage and hormone refractory prostate cancers. One of the DDR, especially Tp53 has been found to be associated with poor prognosis and increased germline mutations. We herein present a quality assurance study to determine feasibility of liquid biopsy for personalized management in veterans for advanced solid malignancies and its clinical impact. Methods Quality assurance documentation from Foundation One (Cambridge MA, NGS) on liquid biopsies performed for the Corporal Michael J. Crescenz Veteran Affairs Medical Center (CMCVAMC) from May 2019 to April 15, 2020 were reviewed. Statistical data for adequacy, cases with notable mutations, frequency and type of mutations of AR, DNA damage repair (DDR) gene and Tp53 were noted. Results A total of 31 liquid biopsies were performed over this time period, of which 29/31 (93.50%) were adequate for evaluation. 23/29 (79.30%) showed notable mutations, in 4/23 (17.39%) guided treatment decisions based on androgen receptor (AR) amplification, and 7/29 (24.1%) of all cases showed DDR gene mutations indicating poor outcome and resistance to the current therapy. Greater than 50% (16/29 (55.7%)) of the veterans with advanced cancers harbored Tp53 mutation, which instills hope and future insight for patient tailored oncologic therapy. Conclusion The minimally invasive liquid biopsy shows a great promise as a diagnostic and prognostic tool in the personalized clinical management of advanced prostate and NSCLC in veteran patient population with unique demographic characteristics. Difference in frequency of the genetic mutations (DDR, TP53, AR) in this cohort provides valuable information for disease progression, lack of response, mechanism of resistance to the implemented therapy and clinical decision making. Precision oncology can be further tailored for this cohort by focusing on DNA repair genes and Tp53 in future for personalized targeted therapy.

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A multicenter, prospective evaluation of a urine-based assay for bladder cancer diagnosis.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e16509 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e16509-e16509

Author(s):

Liang Wang ◽

Yiming Liang ◽

Min Shi ◽

Tonghui Ma ◽

Jianhua Deng ◽

...

Keyword(s):

Bladder Cancer ◽

Negative Predictive Value ◽

Sensitivity And Specificity ◽

Predictive Value ◽

Liquid Biopsy ◽

Gene Mutations ◽

Low Grade ◽

Gold Standard Method ◽

Dna Libraries ◽

Multicenter Prospective Study

e16509 Background: At present, bladder cancer is diagnosed mainly through cystoscopy as the "gold standard" method, which is invasive, costly, and painful for patients. Meanwhile, the current non-invasive liquid biopsy approaches, such as FISH or cytology, still do not show adequate performance in the diagnosis of bladder cancer because of the unsatisfactory sensitivity. Therefore, developing a novel method that performs higher sensitivity and specificity, especially negative predictive value(NPV) is an urgent issue to be addressed and will be very helpful for the clinical application. Methods: From October 2019 to October 2020, we designed a multicenter, prospective study, in which 321 hematuria patients were enrolled, including 218 males and 103 females, and their average age was 56. Based on the final pathological diagnosis, 121 patients were confirmed as bladder cancer and 200 samples were benign urinary diseases. 100ml urine samples were collected from each patient before the endoscopy examination. The Genetron Uro-18 assay, which included a 17 gene mutation panel and the methylation test on ONECUT2, was used in this study. The regions in the panel were selected based on the TCGA database, as well as previous publications. 321 urine DNA libraries were generated using multiplex PCR methods and then sequenced on the Ion S5 System. The CpG-sites on the ONECUT2 gene were detected by bisulfite-specific real-time PCR. Results: In these samples, a total of 205 oncogenic mutations were found in 13 genes in the panel. Mutations on TERT, PIK3CA, FGFR3, and TP53 genes showed significantly higher occurrence. 103 samples were found to be mutation-positive, 92 of which were pathologically confirmed as bladder cancers. When only gene mutations were considered, the sensitivity and specificity of this assay were 76.0% and 94.5%, respectively. The methylation of ONECUT2 had a performance in the test with a sensitivity of 74.4% and specificity of 93.0%. Combining the mutation panel with the ONECUT2 methylation test will improve the sensitivity (86.0%) of this assay, but slightly hampered the specificity (91.0%). The positive predictive value(PPV) and negative predictive value(NPV) of the combination were 85.2% and 91.5%. The sensitivity was as high as 91.5% when low-grade bladder cancer samples were excluded. In contrast, the sensitivity of cytology and FISH tests were only 48.4% and 62.0%. Conclusions: The novel urine-based liquid biopsy assay has excellent performances in the diagnosis of bladder cancer, with sensitivity and NPV reaching 86.0% and 91.5%, which improved significantly than cytology and FISH tests. Thus this assay will be more beneficial for patients with urinary diseases which significantly reduces the current burden of repeat cystoscopies and cytology tests.

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